8TSM | pdb_00008tsm

Crystal structure of chicken Netrin-1 LN LE1-2

PDB DOI: https://doi.org/10.2210/pdb8TSM/pdb

Classification: SIGNALING PROTEIN
Organism(s): Gallus gallus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-08-11 Released: 2024-08-28
Deposition Author(s): Heide, F., Rafiei, F., Stetefeld, J.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.90 Å
R-Value Free:
0.319 (Depositor), 0.318 (DCC)
R-Value Work:
0.312 (Depositor), 0.312 (DCC)
R-Value Observed:
0.312 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Investigation of the dynamic nature of Netrin-1 on dependence receptor signaling

Rafiei, F., Heide, F., Legare, S., Gabir, H., Padilla-Meier, P., Meier, M., Koch, M., Stetefeld, J.

To be published.

Macromolecule Content

Total Structure Weight: 44.68 kDa
Atom Count: 2,846
Modeled Residue Count: 354
Deposited Residue Count: 393
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Netrin-1	A	393	Gallus gallus	Mutation(s): 0 Gene Names: NTN1
UniProt
Find proteins for Q90922 (Gallus gallus) Explore Q90922 Go to UniProtKB: Q90922
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q90922
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.90 Å
R-Value Free: 0.319 (Depositor), 0.318 (DCC)
R-Value Work: 0.312 (Depositor), 0.312 (DCC)
R-Value Observed: 0.312 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.413	α = 90
b = 112.413	β = 90
c = 242.644	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHENIX	phasing
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-08-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2024-08-28
Type: Initial release
Version 1.1: 2024-10-16
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.